Need help with "Cufflinks" tool

Question: Need help with "Cufflinks" tool

3.9 years ago by

Taiwan

joyraj_07 • 10 wrote:

What value does Galaxy use for -max-bundle-frags? I could not find a way of changing this parameter in Galaxy..??

Tool name: Cufflinks
Tool version: 0.0.7
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.7
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/cufflinks

cufflinks • 1.0k views

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modified 3.9 years ago by Martin Čech ♦♦ 4.9k • written 3.9 years ago by joyraj_07 • 10

3.9 years ago by

Jelle Scholtalbers • 360

Germany

Jelle Scholtalbers • 360 wrote:

(According to the specific tool xml - https://toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/file/5346d5eea8b1/cufflinks_wrapper.xml)

You will have to set "Set advanced Cufflinks options:" to "yes" and then you should be able to specify "Maximum number of fragments per locus" which sets the --max-bundle-frags option.

ADD COMMENT • link written 3.9 years ago by Jelle Scholtalbers • 360

Where is this option available "Set advanced Cufflinks options:"? I could not locate it while running cufflinks...

ADD REPLY • link written 3.9 years ago by joyraj_07 • 10

Hopefully both answers help. When you have time, would you please mark either one as accepted (click on the check box next to the reply) this will help others understand how to address the issue and about the pending tool updates. Readers will see both replies and current tool status on Main versus tool shed install of the tool into a local/cloud.

Thanks for helping us to build up a set of Q/A post that are easier for other readers to find. Jen, Galaxy team

ADD REPLY • link written 3.9 years ago by Jennifer Hillman Jackson ♦ 25k

3.9 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

The cufflinks version currently installed on usegalaxy.org does not allow you to change that option. According to the source the default for the installed version is 1 000 000

( '--max-bundle-frags', dest='max_bundle_frags', help='Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 1,000,000' )

We are currently working on updating the usegalaxy tool set. You can see and try the new cufflinks at https://test.galaxyproject.org/ Hopefully soon it will make it to usegalaxy.org

ADD COMMENT • link written 3.9 years ago by Martin Čech ♦♦ 4.9k

Thanks for the information. Can you kindly tell me the host name of test galaxy (whether it is same as galaxy, "main.g2.bx.psu.edu"). I require the host name for FTP upload in test galaxy.

ADD REPLY • link written 3.9 years ago by joyraj_07 • 10

The hostname is the same as the site: ftp://test.galaxyproject.org

ADD REPLY • link written 3.9 years ago by Dannon Baker ♦ 3.7k

As Dannon says. Also note that the hostname of the Main Galaxy is usegalaxy.org and not main.g2.bx.psu.edu anymore (applies to FTP too).

ADD REPLY • link modified 3.9 years ago • written 3.9 years ago by Martin Čech ♦♦ 4.9k

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